The Institute
by NephlimLover437
Summary: Clary's parents are murdered when she is six. She is recruited, to a place that swears she would avenge her family. She is recruited into The Institute; she will stop at nothing to get the answers she needs. But, a certain blonde will show her, who she's really working for.


**I'm glad to be getting back in the swing of things. This story, is kinda like a 'Wanted' and 'Nikita' hybrid, mix up thing. I hope you like this, it is actually another rewrite of a story I had up before, but no one read it so it doesn't really matter. I hope you like, please review and give me feedback.**

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Paint the picture, of the perfect life. You have a loving family, and everything that you could ever ask for. Now sit back, and watch that perfect picture be burned to the ground. Watch the life you had for six short years, be taken away from you. Try watching your child hood thrown in a wood chipper. Add in a short temper, and emotional damage and you get my life.

I remember my life before The Institute, even though I try not to. I had a mother and a father, and I had an older brother named Sebastian. My last night seeing my family, alive we had just gotten back from California, out of the blue, my dad decided to take the family to Disney World **(a/n: or land, I never know which.) **That's just the kind of father he was, when we got back to the house, after looking through the blinds, my dad quickly sent, me upstairs, to put up my bags away, while he held my brother back to talk to him about something. He was thirteen then. Back then I was extremely short, so I had a hard time doing, what most people could do in less than thirty seconds. I finally made it up the stairs and into my bedroom. The way, our upstairs was set up, my brother's room was right across the hall from mine, and my father's office was down the hall. Sometimes me and my brother would go in there, and play games at the bottom of his desk. We were really close like that. I had just, put my last pair of pants, on the hanger and in the closet when, I hard, the sound of glass smashing, and the scream of my mother. I tried, to run out of my bedroom door to see what was going on, but at the same instant, my brother stormed in to the room. He slapped his hand over my mouth, and pushed himself through the door, shutting it behind him. He removed his hand from my mouth, and placed a single finger to his lips, telling me that I still needed to be quiet. He went over, and looked through my blinds, just like my father did. He said a bad word, under his breath, before taking me by my arm and slowly opening my door, and peeping around the corner. He opened the door, wide enough to pull me out and down the hall into my father's office. I heard the sound of voices, but they didn't sound angry, they sounded like they were laughing, until I heard a loud smacking sound, and the scream of my mother. I tried to run, in the direction of the stairs, but Sebastian, jerked my arm not hard enough, to hurt me, but hard enough to get my attention. I followed him, in the office, and he shut the door and locked it behind him.

"'abastain what's going on?" I whispered, as he walked away, in the direction of my dad's bookcase. He lifted one book, of the shelf, and the case slid to the side, revealing my father's safe room. My father, showed it to me once, but I never thought that I'd actually have to use it. He made a hand motion, telling me to get in the room, I stomped my foot like the child I was,

"I'm not getting in there, until you tell me what's going on." Sebastian, groaned,

"Clay, this is not the time, for you to be stubborn." He whisper yelled,

"I just want to know what's-' I heard a loud crash, then a bang, and I ran into my brothers arms. He squeezed my shoulders and gently pushed me into the room. He got down, on his knees so that he was eye level with me, he looked me straight in the eye, he put his hands on my knee.

"Clary, it's just me and you okay, everything is going to be fine." There was a loud, bang nearby, and Sebastian looked up worried.

"I'm going to leave now,-' I looked up quickly, my eyes were starting to glaze over, and it felt like I had a base baseball stuck in my throat.

"No, don't leave me here!" I reached out to him, but he pulled away when he heard angry voices near the room, he pulled away, quickly.

"I'm going to come back for you Clary." He kissed my forehead, he closed, me up in the room, with one last glance, I heard a loud crash, in my dad's office, and what sounded like a lot of people storming in.

I could hear nothing but, mumbles, angry mumbles, crying mumbles, and then I heard glass shattering, and complete silence. I liked the noise, better than no noise, at all. I brought my knees up to my chest, and cried openly. I sat there for what seemed like hours, until I heard more mumbles, they got closer and closer, until I heard them in my dad's office. There was a soft tapping on the door to the safe room. I didn't dare make a sound, I didn't know if it was the mean men or not, I put my hand over my mouth to muffle my cries, and scouted back as far as I possibly could. I didn't know that the door was still part way open, whoever was on the other side slowly, opened it completely, and pointed a gun inside. I screamed, and the guy jumped,

"Shit, guys I found a kid in here." A man in blue said into his shoulder. He put his gun, on his side, and held his hand out to me, smiling sweetly "Are those guys your friends?" I pointed to the group; the guy looked over his shoulder, and looked back at me and smiled,

"Yeah, I guess you could say that." He led me outside, and sat me down on the steps in front of my house, he said,

"Sweetie do you know what happened here tonight." I quickly, shook my head,

"My brother took me and put me in the safe room when my daddy's friends came in." The guy looked sad, but he smiled anyway.

"You wait, right here, I'm going to go and get one of my friends to keep you company." He walked away quickly, I thought I could see his eyes, getting all misty, like my mom's did when ever my dad gave her one of his just because gifts. A few minutes later, a nice, looking lady came and sat down in front of me.

"Hey sweetheart." She handed me a small piece of candy, I whispered out a small 'hi'

"So you don't know what happened here tonight do you?" I took, the wrapper off and put, the candy in my mouth,

"My brother, put in me in the safe room when, my daddy's friends came over. Do you know where my family is?" I cocked my head to the side; the woman took, a deep breath, and smiled weakly,

"Honey those people weren't your fathers friends. You father is gone, honey I'm sorry."

"Gone? Gone where?" I don't why I asked, because I already knew what she meant, but I thought maybe- I don't maybe I just didn't want to believe it.

I, her silence was enough for me, my parents told me about, the season when everything, has to leave. But I never thought I would have, to learn about this with my family. I looked, down at my knees, that baseball was back in my throat, I stood and took off up the stairs.

"Somebody get her!" I heard the woman behind me yell. I pushed, through all the people in blue, till I got to the middle of the circle, there was a black, bag and blood everywhere. There was someone taking pictures, because I walked in, in the middle of a flash. For a couple of seconds, all I saw was multi-colored dots. When my vision came back I saw that my father was in the bag, my breath became ragged, I screamed,

"Daddy! Wake up." I fell to my knees in front of him, sinking into a pool of blood I was quickly dragged away, kicking and screaming.

"What happened, to my parents, what happened? Where is my brother! Where's my mommy! Someone tell me what happened" I cried, as they placed my in the back of a car. I loss everyone that day, the people in blue didn't even know I had a brother. Everything after that was a blur. I was brought into the police station, and forced to sit in a small room, while people continuously asked me questions. I said the same thing over and over- that I didn't know- but they wouldn't leave me alone. After, a while, the people and blue told me to sit on a bench, and wait for someone to take me to my new home. I told them I didn't want a new home, but they didn't listen to me. Soon, a woman came into the police office, and signed some papers and walked over to me.

"Hi, honey. I'm going to be taking you to your new home, is that okay?" she asked, in a voice that sounded like honey.

"But I want my old home." I whispered, by then I had just given up. She nodded,

"I'm sorry sweetie, but I'll try my best to make you happy." The car ride was uncomfortable; I sat with the little bag that the police packed for me, in my lap. The house was small, but it looked homey from the outside. The inside made me feel cold and alone, there were already six-kids, there I was the second youngest, the other girl looked to be about nine. When I first got there I didn't talk to anyone, I had nothing to say. Someday I would get home from school and I wouldn't even eat. I went from being the happiest kid in the world, to the most miserable, to the little girl who was pissed off all the time, for no clear reason. I got into fights at school, and with other girls in the house. I dislocated one girls, arm all because, she used the last of the milk, and left the empty container in the fridge. Apparently that's not a good enough reason to break someone's arm. I had a stash, of growing rage, and every time I thought about my parents, it just grew bigger and bigger. I had a smart mouth and dirty 'language' as people liked to call it. I didn't see it that way, I wanted answers, and the police weren't giving me any. They closed the case on the murder of my father and the disappearances of my mother and brother. They said they didn't have enough information, and that the case had been open for too long, and they ran out of leads. I told them, they were full of shit. I didn't give a rats ass, that the case was seven years old. I didn't care that they ran out of leads, I wanted answers.

"I'm really sorry Clair." Said one cop, who obviously didn't care enough to remember my name; I saw red, that was the last straw, from the beginning these people didn't give a damn; I stood, and threw the chair I was sitting in across the table, at the cops face, I crawled across the table, in poked my finger in his chest,

"My name is Clarissa, you fat jack ass, and don't apologize because you and me both know you don't give a damn!" I was pulled of the table, by the same lady that told me about my parents. She pushed me up against, a wall

"Clarissa, calm down or we'll be forced to take you into custody." I scowled deeply and spit into her face,

"Fuck you." She raised a hand, and hit me across the face, knocking me to the ground

"Someone get her out of here." I was hauled to my feet, and, my right, arm was roughly twisted behind my back. The officer pushed me against a wall, smashing, my face into wall. He read me my rights, while another officer, put the hand cuffs on me.

"Comfy?" it was the officer I hit in the face, I jerked my shoulder back in trying to hit him again,

"Go, fuck yourself douchdick." He tightened the cuffs, on my wrist and forcibly led me out of the house; I was forced to call home for the last seven years. I really had no friends in the house, I never talked, and when I did I was always snapping on someone. No, one cared when he saw me, being led out of the house in cuffs, including myself- I had no one to live for anymore. My foster mom, sat at the door, with tears in her eyes. She was the only one that I actually talked to. She knew, what was going on with me. I was pushed into a car, into and later, thrown into a cell, on my face, busting my nose.

"Hurts don't it." said the officer that I hit. I ignored him and picked myself up off the ground, my nose was bleeding all over my shirt, but I didn't care. I didn't care about anything. With the chair in my eyes, in my eyes, I had just gone from one prison to another. I sat in the back of my cell, and cried silently. I spent only a few hours, in a cell, before the cage was opened, and an officer was telling me that I was being released. I had no family, and I know Maryse couldn't afford to get me out; I had no idea who would actually post bail for me. I walked out, to see a tall woman in a pants suit, with her back facing me. I cleared my throat to get her attention; she turned around, and raised an eyebrow.

"Do I know you?" I crossed my arms, over my chest and leaned back against, the desk of a police officer. She raised a perfectly manicured hand out for me to shake; I looked, down at it, and looked back at her without taking it, I'm not in civility.

"I'm Celine Herondale normally, when someone holds out her hand, you're supposed to shake it." I rolled my eyes, but still didn't shake her hand,

"I'm supposed to do a lot of things, now who are you." she slowly dropped her hand; her smile was replaced with a smirk.

"Your attitude is going to have to be the first thing we'll have to work on." she turned and walked away, like he just knew I would follow him. My curiosity got the best of me and I did. I walked quickly behind him, until he got into the back of a car, there was parked outside, she opened the door and slid into the car, then looked back up at me,

"Are you going to get in or not?" she rolled her eyes, and looked up at me, exasperated

"Where are you talking me?" I was starting to get nervous,

"I'm going to get you some answers, I know all about your pass, and how the police closed the case, on your parents. I'm a friend here to help." I still didn't answer my question,

"You didn't answer my question. Where are we going?" I tried again. She sighed out,

"I'm taking you to The Institute. Either, you're going to kiss your pass goodbye and get in this car, or you can find your way back to your foster home." Against my better judgment, I ducked my head, and got into the car. I wanted answers.

I would do whatever it took, to avenge my parents, and find my brother.

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Getting, in that car was the worst and best decision I ever made. Celine first took me to an airport. She told me I was to board a plane to New York and there would be a car waiting for me there, and I would be briefed on my way to my destination. It was all a lot to take in, but I nodded my head anyway and pretended like I knew what was going on. I stepped out of the car and was quickly put on the plane; something about it wasn't safe for anyone to see me. I had the plane, to myself, but I hated to be alone, so it didn't do wonders for me. Everything moved too fast, as soon as the plane door descended, I was rushed out and into another car. This one was occupied, by a small dark haired girl.

_***Flashback***_

"_Hi, you must be Clarissa; I'm Isabelle Lightwood here to brief you." She held her hand out to me, and I took it shyly. I didn't like physical contact, anymore. _

_ "Nice, to meet you-' I whispered '- are you going to tell me what The Institute, is all about?" she smiled slightly and nodded her head, _

_ "Yes, I'm going to tell you what The Institute is all about, we have a pretty long drive, so we should have enough time to cover everything." she, knocked, on the window, telling the driver to go. _

_ "The Institute is a black-ops branch of the government. We are still unknown to the general public, for the time being anyway- you really never know what could happen." That didn't explain why I was here, _

_ "Why am I here Is__belle?"_

_ "The Institute recruits people with troubled backgrounds and no answers. Most of the time only criminals and convicts are recruited. We erase their past and give them basically a new life. The head of The New York Institute, decides who gets recruited or not. But, that doesn't answer your question, you are here for reasons that I can't really tell you. My job is to take you to the leader. But, I can answer any other questions for you." She leaned back in here seat, _

_ "It can't be this simple, what's the catch?" I may have grown up naive, but I'm not an idiot. _

_ "If, you chose to be a part of The Institute, you will be a trained assassin. Our job is carrying out missions that are given to us. Your training will almost as soon as you get settled in." She said_

_ "Well how is this going to tell me about my family?" This was way too confusing, _

_ "When the time is right." She said simply, I rolled my eyes, and rested my head back against the seat. The car stopped not long after that, Isabelle stepped out of the car first, and then I did. We were standing in front of an old abandoned church/ rape warehouse type thing. I turned to Isabelle in confusion _

_ "Welcome to the Institute."_

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**Please review/ give me feedback, and check out my other stories. **

**-Shay**

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IF ANYONE WANTS TO BE A **TEMPORARY **BETA; WHILE MINE IS ON VACATION, PLEASE LET ME KNOW, AS SOON AS YOU CAN!


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